Cycles Not Rendering Specified Samples
You appear to have a per-renderlayer sample override limit set in Properties > Render layers > Layer:



To avoid this, either set the sample override to 0 in the appropriate renderlayers, or tell blender to ignore per-renderlayer sample overrides in Properties > Render settings > Sampling:





Note that you have Square Samples enabled. This means that blender will use the number of samples you specified2. The total number of samples is displayed below:



(TBH I don't really see the point of this feature..)

Also 500 bounces are almost never needed. Higher numbers of bounces give diminishing returns, and I doubt there will be much visual difference between 6 bounces and 100 bounces in a fairly diffuse scene such as yours.